Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtttgtttctgtaaccttccgttaaatttgtgggatcgaattttcattcataaattagttccatgaattgtgttgttttgattgtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGTTCAAATTTCCCGAGAACAGTGTCGAGCTTTATGCTGAGAAGGTCAACAA

Basic information

species Glycine max
transcript GLYMA09G28440.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G28440.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G31610.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgcgtttgtttctgtaaccttccgttaaatttgtgggatcgaattttcattcataaattagttccatgaattgtgttgttttgattgtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGTTCAAATTTCCCGAGAACAGTGTCGAGCTTTATGCTGAGAAGGTCAACAA
    || ||||| | | | | |   ||   | | | |  |   | | |  |||   |  |  |  |   || |||   |||||            |||||||||||| ||||||||||||||| | || ||  | || |||||||| ||||| ||||| |   ||||||| ||||| |||||||||||||| |||||
----gtatgtttgtttgatcatttcttctctctttcgattttgaatgtgtttcgagatctgatatcg-aaaatgttgggtttt------------agGTGAGAAGGGGAGGAGAATTAGGGAATTGACATCTCTTGTCCAGAAGAGATTCAAGTTTCCAGTTGACAGTGTTGAGCTCTATGCTGAGAAGGTTAACAA

upper sequence: GLYMA09G28440.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G35530.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgcgtttgtttctgtaaccttccgttaaatttg-tgggatcgaattttcattcataaattagttccatgaattgtgttgttttgattgtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGTTCAAATTTCCCGAGAACAGTGTCGAGCTTTATGCTGAGAAGGTCAACAA
    || ||||  || |   || ||||||  ||| |  |||   |  ||  ||  |   |   |   || |||| || || ||   |  |   | ||||||||||||||||||| ||||||||| | || ||  | || || ||||| |||||||||||  || ||||||| ||||||||||||||||||||    ||
----gtatgttggtgca--ttttcgttaaccttgctctgattcgacctttttttgtt--tctatgatatcaatt-tgatgattctctgtttggtttagGTGAGAAGGGAAGGAGGATTAGGGAATTGACATCTCTTGTACAAAAGAGATTCAAATTTCCTCAGGACAGTGTTGAGCTTTATGCTGAGAAGGTTGCTAA

upper sequence: GLYMA09G28440.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G53870.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgcgtttgtttctgtaaccttccgttaaatttgtgggatcgaattttcattcataaattagttccatgaattgtgttgttttgattgtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGTTCAAATTTCCCGAGAACAGTGTCGAGCTTTATGCTGAGAAGGTCAACAA
    || ||||| ||  | ||||     |  ||     |||   | |||  | |||   ||||       | |||    ||| |||||||| |  |||||||||||| ||||||||||||||| | || ||  | || |||||||| ||||| ||||| |   ||||||| ||||||||||| |||||||| |||||
----gtatgtttttg--atcttc----gagctt----aatcatttcttctattatacggtagt------gactgtaaaattt-gattgtat-ttcagGTGAGAAGGGGAGGAGAATTAGGGAATTGACTTCCCTTGTTCAGAAGAGATTCAAGTTTCCAGTTGACAGTGTTGAGCTTTATGCCGAGAAGGTTAACAA

upper sequence: GLYMA09G28440.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv11s0016g01380.t01 (Vitis vinifera), 3'ss of exon 2
gtgcgtttgtttctgtaaccttccgttaaatttgtgggatcgaattttcattcataaattagttccatgaattgtgttgttttgattgta-tatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGTTCAAATTTCCCGAGAACAGTGTCGAGCTTTATGCTGAGAAGGTCAACAA
       || |||  |  | ||   |   |||  || | |||  |||      ||   || |||   ||| |    || |||   || |    | |||||||||| || ||||||||||| ||| | || || || || || ||| | ||||| ||||| ||||||||||| ||| | ||||| ||||| ||||||||
------gtgattcaatggctttgatt---attcttgagttcgcgtttcag---atttgttggttttctgactctccttttttgctttttggcttttagGTGAGAAAGGGAGGAGAATTAGAGAATTGACGTCCGTTGTACAAAAGCGATTCAAGTTTCCTGAGAACAGTGTGGAGTTGTATGCCGAGAAAGTCAACAA

upper sequence: GLYMA09G28440.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S127_74V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------gtgcgtt-tgtttctgtaaccttccgttaaatttgtgggatcgaattttcattcataaattagttcca---------tgaattgtgttgttttgattgtatat--atagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGTTCAAATTTCCCGAGAACAGTGTCGAGCTTTATGCTGAGAAGGTCAACAA
                           |||| | ||  ||||  |   |  |  | | ||  ||  |    | ||    |  |  | | ||             | ||||   |    ||| ||        |||||||||||||| | || || |||||||| ||||| ||||| |||||||||||  | || || |||   | ||| ||| | || || |||||||| |||||
gtgagtctcttggctgcactgacattatgcgctatggatctggtagtctttgagataattagggttttttctctttggccggaggtgaatttgcgggggtagtcggattgaagtagggtgactgctccctggtagGTGAGAAGGGACGAAGGATCAGGGAACTGACCTCCGTGGTACAGAAGAGGTTTCAGTTCCCGGAGGGTACTGTGGAGTTGTACGCCGAGAAGGTGAACAA

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|23058305|gb|BU578303.1|BU578303
EST:     GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCG                         GTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
genomic: GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCGgtgcgtttgt ... gtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
EST: gi|12496516|gb|BG047103.1|BG047103
EST:     GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCG                         GTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
genomic: GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCGgtgcgtttgt ... gtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
EST: gi|5677916|gb|AI939046.1|AI939046
EST:     GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCG                         GTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
genomic: GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCGgtgcgtttgt ... gtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
EST: gi|33389542|gb|CA852749.1|CA852749
EST:     GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCGAGCCGTTCTCG                         GTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
genomic: GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCGgtgcgtttgt ... gtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
EST: gi|4291003|gb|AI441699.1|AI441699
EST:     ATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCNCGTTCT-G                         GTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGG
genomic: ATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGC-CGTTCTCGgtgcgtttgt ... gtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGG
EST: gi|12497107|gb|BG047401.1|BG047401
EST:     GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCG                         GTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCANAAGAGGT
genomic: GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCGgtgcgtttgt ... gtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
EST: gi|24205365|gb|BU964618.1|BU964618
EST:     GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCG                         GTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
genomic: GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCGgtgcgtttgt ... gtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
EST: gi|8283729|gb|BE021288.1|BE021288
EST:     GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCG                         GTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
genomic: GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCGgtgcgtttgt ... gtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
EST: gi|120496311|gb|EH224478.1|EH224478
EST:     GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCG                         GTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
genomic: GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCGgtgcgtttgt ... gtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
EST: gi|4290831|gb|AI437533.1|AI437533
EST:     GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCG                         GTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
genomic: GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCGgtgcgtttgt ... gtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
EST: gi|254325495|gb|GR838376.1|GR838376
EST:     GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCG                         GTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
genomic: GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCGgtgcgtttgt ... gtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
EST: gi|192305912|gb|FG995462.1|FG995462
EST:     GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCG                         GTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
genomic: GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCGgtgcgtttgt ... gtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
EST: gi|120496331|gb|EH224498.1|EH224498
EST:     GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCG                         GTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
genomic: GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCGgtgcgtttgt ... gtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
EST: gi|151406004|gb|EV275819.1|EV275819
EST:     GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCG                         GTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
genomic: GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCGgtgcgtttgt ... gtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
EST: gi|213592479|gb|DB971635.1|DB971635
EST:     GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCG                         GTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
genomic: GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCGgtgcgtttgt ... gtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
EST: gi|192305913|gb|FG995463.1|FG995463
EST:     GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCG                         GTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
genomic: GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCGgtgcgtttgt ... gtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
EST: gi|14990868|gb|BI316541.1|BI316541
EST:     GATGCGCACCGAGATTATCATCAGAGCCACCATAACCCAAGCCGTTCTCG                         GTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
genomic: GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCGgtgcgtttgt ... gtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
EST: gi|151409012|gb|EV278820.1|EV278820
EST:     GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCG                         GTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
genomic: GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCGgtgcgtttgt ... gtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
EST: gi|298179211|gb|HO027682.1|HO027682
EST:     GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCG                         GTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
genomic: GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCGgtgcgtttgt ... gtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
EST: gi|20814979|gb|BQ299457.1|BQ299457
EST:     GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCG                         GTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
genomic: GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCGgtgcgtttgt ... gtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
EST: gi|21889395|gb|BQ742608.1|BQ742608
EST:     GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCG                         GTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
genomic: GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCGgtgcgtttgt ... gtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
EST: gi|21889541|gb|BQ742754.1|BQ742754
EST:     GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCG                         GAGAGAACGGAAGGAGAATTAGGGAACTTACCTCACTGGTGCAGAAGAGGT
genomic: GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCGgtgcgtttgt ... gtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
EST: gi|298164138|gb|HO013783.1|HO013783
EST:     GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCG                         GTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
genomic: GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCGgtgcgtttgt ... gtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
EST: gi|9564213|gb|BE473722.1|BE473722
EST:     GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCG                         GTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT
genomic: GATGCGCACCGAGATTATCATCAGAGCCACCAGAACCCAAGCCGTTCTCGgtgcgtttgt ... gtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattttcattcataaattagttccatgaattgtgttgttttgattgtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGTTCAAATTTCCCGAGAACAGTGTCGAGCTTTATGCTGAGAAGGTCAACAA
                                     ttttgat  putative branch site (score: 4)
                                     ttttgattgtatatat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtttgtttctgtaaccttccgttaaatttgtgggatcgaattttcattcataaattagttccatgaattgtgttgttttgattgtatatatagGTGAGAAGGGAAGGAGAATTAGGGAACTTACCTCAGTGGTGCAGAAGAGGTTCAAATTTCCCGAGAACAGTGTCGAGCTTTATGCTGAGAAGGTCAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG